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Soil organisms are a crucial part of the terrestrial biosphere. Despite their importance for ecosystem functioning, few quantitative, spatially explicit models of the active belowground community currently exist. In particular, nematodes are the most abundant animals on Earth, filling all trophic levels in the soil food web. Here we use 6,759 georeferenced samples to generate a mechanistic understanding of the patterns of the global abundance of nematodes in the soil and the composition of their functional groups. The resulting maps show that 4.4 ± 0.64 × 1020 nematodes (with a total biomass of approximately 0.3 gigatonnes) inhabit surface soils across the world, with higher abundances in sub-Arctic regions (38% of total) than in temperate (24%) or tropical (21%) regions. Regional variations in these global trends also provide insights into local patterns of soil fertility and functioning. These high-resolution models provide the first steps towards representing soil ecological processes in global biogeochemical models and will enable the prediction of elemental cycling under current and future climate scenarios., This research was supported by a grant from DOB Ecology to T.W.C., a grant from the Netherlands Organization for Scientific Research (grant 016.Veni.181.078) to S.G., grants from NSF (OPP 1115245, 1341736, 0840979) to B.J.A., by a Ramon y Cajal fellow award (RYC-2016-19939) to R.C.H., a grant from UNEP & Global Environment Facility to J.E.C., a grant from NERC (NE/M017036/1) to T.C., a grant from FAPEMIG/FAPESP/VALE S.A.(CRA-RDP-00136-10) to L.B.C., through the strategic programme UID/BIA/04050/2013 (POCI-01-0145-FEDER-007569) awarded to S.R.C., a grant from CNPq PROTAX (562346/2010-4) to J.M.d.C.C., a grant from DFG (CRC990) to V.K. and S.S., a grant from the MSHE of Russia (AAAA-A17-117112850234-5) to A.A.K., grants from the Chinese Academy of Sciences (XDB15010402) and the National Natural Science Foundation of China (41877047) to Q.L., grants from the National Natural Science Foundation of China (31330011, 31170484) to W.L., grants from NERC (NE/M017036/1) to M.M., grants from the Spanish Ministry of Innovation (CGL2009-14686-C02-01/ 02, CGL2013-43675-P) to J.A.R.M., grants from NSF (DEB-0450537, DEB-1145440) to P.M., T.O.P. and K. Powers, grants from the German Academic Exchange Service (PKZ 91540366) and NAFOSTED (106.05 – 2017.330) to T.A.D.N., by an ARC Discovery project (DP150104199) to U.N.N., by the National Key Research and Development Program of China (2016YFC0502101) and the National Natural Science Foundation of China (31370632) to K. Pan, a grant from the Natural Environment Research Council (NERC) to D.G.W., a grant from BAPHIQ (106AS-9.5.1-BQ-B3) J.-i.Y. The James Hutton Institute receives financial support from the Scottish Government Rural and Environment Science and Analytical Services (RESAS) division. Investigations in northwest Russia were carried out under state order for IB KarRC RAS and are partially supported by the Russian Foundation for Basic Research (18-34-00849). We thank E. Clark and A. Orgiazzi for review of the manuscript; and R. Bouharroud, Z. Ferji, L. Jackson and E. Mzough for providing data.

International audience; In perennial plants, the release of bud dormancy, with subsequent flowering, resembles the vernalization process of Arabidopsis thaliana and cereals. Especially for perennial crops from temperate regions, dormancy is an important adaptive trait for both survival and growth. Exposure to sufficient chilling during winter dormancy ensures the normal phenological traits in subsequent growing periods. Here, we compile research data on mechanisms controlling the overlapping developmental processes that define dormancy induction, maintenance and release, bud burst and flowering. Recent findings highlight the relevance of genome-wide epigenetic modifications related to dormancy events, and more specifically the epigenetic regulation of DORMANCY-ASSOCIATED MADS-box, FLOWERING LOCUS C and FLOWERING LOCUS T genes, key integrators of vernalization effectors on flowering. The roles of plant growth regulators in controlling bud break and flowering are discussed in relation to epigenetic mechanisms. A growing body of knowledge demonstrates that epigenetic regulation plays a key role in these processes in perennial horticultural and forestry plants. We discuss the most relevant molecular and genomics research that contribute to better understanding of the dormancy process and pave the way to precise manipulation of dormancyrelated horticultural traits, such as flowering time. Finally, some of the challenges for further research in bud dormancy and consequences in agriculture are discussed within the context of global climate change.

International audience; Biological invasions are rapid evolutionary events in which populations are usually subject to a founder event during introduction followed by rapid adaptation to the new environment. Molecular tools and Bayesian approaches have shown their utility in exploring different evolutionary scenarios regarding the invasion routes of introduced species. We examined the situation for the tobacco aphid, Myzus persicae nicotianae, a recently introduced aphid species in Chile. Using seven microsatellite loci and approximate Bayesian computation, we studied populations of the tobacco aphid sampled from several American and European countries, identifying the most likely source populations and tracking the route of introduction to Chile. Our population genetic data are consistent with available historical information, pointing to an introduction route of the tobacco aphid from Europe and/or from other putative populations (e.g. Asia) with subsequent introduction through North America to South America. Evidence of multiple introductions to North America from different genetic pools, with successive loss of genetic diversity from Europe towards North America and a strong bottleneck during the southward introduction to South America, was also found. Additionally, we examined the special case of a widespread multilocus genotype that was found in all American countries examined. This case provides further evidence for the existence of highly successful genotypes or ‘superclones’ in asexually reproducing organisms

Photosynthesis, flavonoid biosynthesis, tricarboxylic acid cycle, and ribosome biogenesis genes were significantly regulated during apple bud dormancy progression. PRE1-like and FLC-like genes are master candidates for control of bud phenology.Apple production depends on the fulfilment of a chilling requirement for bud dormancy release. Insufficient winter chilling results in irregular and suboptimal bud break in the spring, with negative impacts on apple yield. Trees from apple cultivars with contrasting chilling requirements for bud break were used to investigate the expression of the entire set of apple genes in response to chilling accumulation in the field and controlled conditions. Total RNA was analysed on the AryANE v.1.0 oligonucleotide microarray chip representing 57 000 apple genes. The data were tested for functional enrichment, and differential expression was confirmed by real-time PCR. The largest number of differentially expressed genes was found in samples treated with cold temperatures. Cold exposure mostly repressed expression of transcripts related to photosynthesis, and long-term cold exposure repressed flavonoid biosynthesis genes. Among the differentially expressed selected candidates, we identified genes whose annotations were related to the circadian clock, hormonal signalling, regulation of growth, and flower development. Two genes, annotated as FLOWERING LOCUS C-like and MADS AFFECTING FLOWERING, showed strong differential expression in several comparisons. One of these two genes was upregulated in most comparisons involving dormancy release, and this gene's chromosomal position co-localized with the confidence interval of a major quantitative trait locus for the timing of bud break. These results indicate that photosynthesis and auxin transport are major regulatory nodes of apple dormancy and unveil strong candidates for the control of bud dormancy.

A propriedade agrícola é cada vez mais reconhecida como um objeto de estudo complexo. Isso se torna importante quando nela se intervém para fornecer um conselho de orientação ou uma ajuda à gestão, ou, num quadro mais amplo, no âmbito de um plano de desenvolvimento rural. Nos estabelecimentos leiteiros das frentes pioneiras da Amazônia, cuja diversidade de funcionamento é particularmente marcante, a modelagem da diversidade, graças à construção de tipologias, representa uma etapa importante para a organização do desenvolvimento agrícola. A partir do caso das explorações leiteiras no município de Uruará, na frente pioneira da Transamazônica, foram identificados cincos principais tipos de sistemas de produção de leite e trajetórias desses. A combinação dessas duas tipologias levou a caracterizar as principais dinâmicas possíveis dentro da diversidade dos sistemas leiteiros, representando as principais evoluções entre os tipos de propriedades. Os resultados salientam a importância de fatores socioeconômicos na implementação e desenvolvimento da atividade leiteira. Nesse contexto, as propostas formuladas devem favorecer a integração da produção leiteira, a sua permanência e a melhoria das condições de produção., The farm is each time more recognized as an object of complex study. This if becomes important when the farm is the object to supply an advice of orientation or an aid to the management, or the scope of a plan of agricultural development. For the dairy farms in agricultural borders of the Amazon, characterized by an important diversity of operation mode, the modeling of the diversity with the elaboration of typologies is an important stage for the organization of the agricultural development. From the case of dairy farms in Uruará municipio, situated on the Transamazonian frontier region, five main types of systems of milk production and theirs trajectories had been identified. Associating these two typologies, it was possible to identify the main dynamics within the diversity of the dairy systems, which represent principal evolutions between groups of farms. The results emphasize the importance of socioeconomics factors for the installation and the development of the dairy production. Inside this context, proposals can be formulated to promote the beginning of the dairy production, its stability and the improvement of the conditions of production.

International audience; Aim: Macroinvertebrates comprise a highly diverse set of taxa with great potential as indicators of soil quality. Communities were sampled at 3,694 sites distributed world-wide. We aimed to analyse the patterns of abundance, composition and network characteristics and their relationships to latitude, mean annual temperature and rainfall, land cover, soil texture and agricultural practices. Location: Sites are distributed in 41 countries, ranging from 55 degrees S to 57 degrees N latitude, from 0 to 4,000 m in elevation, with annual rainfall ranging from 500 to >3,000 mm and mean temperatures of 5-32 degrees C. Time period: 1980-2018. Major taxa studied: All soil macroinvertebrates: Haplotaxida; Coleoptera; Formicidae; Arachnida; Chilopoda; Diplopoda; Diptera; Isoptera; Isopoda; Homoptera; Hemiptera; Gastropoda; Blattaria; Orthoptera; Lepidoptera; Dermaptera; and "others". Methods: Standard ISO 23611-5 sampling protocol was applied at all sites. Data treatment used a set of multivariate analyses, principal components analysis (PCA) on macrofauna data transformed by Hellinger's method, multiple correspondence analysis for environmental data (latitude, elevation, temperature and average annual rainfall, type of vegetation cover) transformed into discrete classes, coinertia analysis to compare these two data sets, and bias-corrected and accelerated bootstrap tests to evaluate the part of the variance of the macrofauna data attributable to each of the environmental factors. Network analysis was performed. Each pairwise association of taxonomic units was tested against a null model considering local and regional scales, in order to avoid spurious correlations. Results: Communities were separated into five clusters reflecting their densities and taxonomic richness. They were significantly influenced by climatic conditions, soil texture and vegetation cover. Abundance and diversity, highest in tropical forests (1,895 +/- 234 individuals/m(2)) and savannahs (1,796 +/- 72 individuals/m(2)), progressively decreased in tropical cropping systems (tree-associated crops, 1,358 +/- 120 individuals/m(2); pastures, 1,178 +/- 154 individuals/m(2); and annual crops, 867 +/- 62 individuals/m(2)), temperate grasslands (529 +/- 60 individuals/m(2)), forests (232 +/- 20 individuals/m(2)) and annual crops (231 +/- 24 individuals/m(2)) and temperate dry forests and shrubs (195 +/- 11 individuals/m(2)). Agricultural management decreased overall abundance by

International audience; Cereal crops are frequently affected by toxigenic Fusarium species, among which the most common and worrying in Europe are Fusarium graminearum and Fusarium culmorum. These species are the causal agents of grain contamination with type B trichothecene (TCTB) mycotoxins. To help reduce the use of synthetic fungicides while guaranteeing low mycotoxin levels, there is an urgent need to develop new, efficient and environmentally-friendly plant protection solutions. Previously, F. graminearum proteins that could serve as putative targets to block the fungal spread and toxin production were identified and a virtual screening undertaken. Here, two selected compounds, M1 and M2, predicted, respectively, as the top compounds acting on the trichodiene synthase, a key enzyme of TCTB biosynthesis, and the 24-sterol-C-methyltransferase, a protein involved in ergosterol biosynthesis, were submitted for biological tests. Corroborating in silico predictions, M1 was shown to significantly inhibit TCTB yield by a panel of strains. Results were less obvious with M2 that induced only a slight reduction in fungal biomass. To go further, seven M1 analogs were assessed, which allowed evidencing of the physicochemical properties crucial for the anti-mycotoxin activity. Altogether, our results provide the first evidence of the promising potential of computational approaches to discover new anti-mycotoxin solutions

La conservation des ressources génétiques forestières garantit le maintien d'une diversité élevée, donc l'adaptation des espèces forestières tropicales aux conditions écologiques actuelles et futures. Elle nécessite d'élaborer des stratégies appropriées à l'aménagement des forêts et, pour cela, d'appréhender tout d'abord le niveau et la structure de la diversité génétique, de comprendre et prévoir ensuite sa dynamique. C'est dans cet esprit qu'une collaboration a été entreprise entre la Guyane française et le Brésil, malgré les différences existant entre les deux systèmes de gestion. À partir de résultats sur les parcelles expérimentales de Paracou (Guyane) et Tapajós (Brésil), un ensemble intégré d'outils a été élaboré, allant d'une base de données et d'utilitaires cartographiques jusqu'à un modèle de simulation de la dynamique des structures génétiques et à un logiciel de gestion.

The coconut mite, Aceria guerreronis Keifer, is one of the main pests of the coconut tree (Cocos nucifera L.) worldwide. Its control is mainly based on the use of acaricides. However, due to the habitat of this pest mite, which is protected by fruit bracts that act as a physical barrier, chemical control is often inefficient. Thus, natural enemies have been studied as an alternative to acaricides. We evaluated the functional and numerical responses of Amblyseius aerialis (Muma) to increasing densities of A. guerreronis (40, 80, 160, 240 and 360) and additionally the oviposition rates of the phytoseiid A. aerialis over 11 days on different food sources: coconut pollen, A. guerreronis and a mix of pollen and A. guerreronis. Our results showed that Amblyseius aerialis showed a type III functional response, where prey consumption increasing as the density of A. guerreronis increased, with a maximum consumption of up to 175 prey per predator. All the prey densities allowed female oviposition. The number of eggs laid by A. aerialis increased with increasing prey density and stabilized between 240 and 360 A. guerreronis individuals, with an average oviposition of 1.7 eggs/female. Furthermore, our results showed that all the food sources (coconut pollen, A. guerreronis and a mix of pollen and A. guerreronis) supported oviposition. The mean oviposition was approximately 1.5 eggs/female on all the food sources. Our study suggests that A. aerialis can be effective in the biological control of A. guerreronis. However, further studies are needed to investigate whether A. aerialis can explore the habitat of A. guerreronis and if that prey can support the development of immature stages and the reproduction of A. aerialis. Made available in DSpace on 2022-01-10T18:00:36Z (GMT). No. of bitstreams: 1 Acarologia-2022-62-27-35.pdf: 1574877 bytes, checksum: a112d0048962fcea11e67719d957ba31 (MD5) Previous issue date: 2022

Made available in DSpace on 2019-10-06T15:42:46Z (GMT). No. of bitstreams: 0 Previous issue date: 2019-04-15 Agropolis Fondation Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Information about population structure and genetic relationships within and among wild and brazilian Coffea arabica L. genotypes is highly relevant to optimize the use of genetic resources for breeding purposes. In this study, we evaluated genetic diversity, clustering analysis based on Jaccard’s coefficient and population structure in 33 genotypes of C. arabica and of three diploid Coffea species (C. canephora, C. eugenioides and C. racemosa) using 30 SSR markers. A total of 206 alleles were identified, with a mean of 6.9 over all loci. The set of SSR markers was able to discriminate all genotypes and revealed that Ethiopian accessions presented higher genetic diversity than commercial varieties. Population structure analysis indicated two genetic groups, one corresponding to Ethiopian accessions and another corresponding predominantly to commercial cultivars. Thirty-four private alleles were detected in the group of accessions collected from West side of Great Rift Valley. We observed a lower average genetic distance of the C. arabica genotypes in relation to C. eugenioides than C. canephora. Interestingly, commercial cultivars were genetically closer to C. eugenioides than C. canephora and C. racemosa. The great allelic richness observed in Ethiopian Arabica coffee, especially in Western group showed that these accessions can be potential source of new alleles to be explored by coffee breeding programs. Instituto Agronômico do Paraná (IAPAR), Rodovia Celso Garcia Cid, 375 Km Centro de Ciências Biológicas Área de Genética e Biologia Molecular Universidade Estadual de Londrina (UEL), CP 10.011 CIRAD UMR AGAP AGAP Univ. Montpellier CIRAD INRA INRIA Montpellier SupAgro Departamento de Agronomia Universidade Estadual de Londrina (UEL), CP 6001 Instituto Agronômico do Paraná (IAPAR) Mestrado em Agricultura Conservacionista, CP 481 Instituto de Biociências de Rio Claro Universidade Estadual Paulista (UNESP) Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA Café) Laboratório de Biotecnologia de Plantas – IAPAR Embrapa Café, Rodovia Celso Garcia Cid, 375 km Instituto de Biociências de Rio Claro Universidade Estadual Paulista (UNESP)

Made available in DSpace on 2019-10-05T15:49:12Z (GMT). No. of bitstreams: 0 Previous issue date: 2019-03-01 Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Empresa Brasileira de Pesquisa Agropecuaria (Embrapa Pecuaria Sudeste) Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) National Priority Program for Animal and Plant Health, Ministry of Agriculture, Cuba Water buffalo is important livestock in several countries in the Latin American and Caribbean regions. This buffalo species can be infected by tick-borne hemoparasites and remains a carrier of these pathogens which represent a risk of infection for more susceptible species like cattle. Therefore, studies on the epidemiology of tick-borne hemoparasites in buffaloes are required. In this study, the prevalence of Babesia bovis, Babesia bigemina, and Anaplasma marginale were determined in water buffalo herds of western Cuba. To this aim, a cross-sectional study covering farms with large buffalo populations in the region was performed. Eight buffalo herds were randomly selected, and blood samples were collected from 328 animals, including 63 calves (3-14months), 75 young animals (3-5years), and 190 adult animals (>5years). Species-specific nested PCR and indirect ELISA assays were used to determine the molecular and serological prevalences of each hemoparasite, respectively. The molecular and serological prevalence was greater than 50% for the three hemoparasites. Differences were found in infection prevalence among buffalo herds, suggesting that local epidemiological factors may influence infection risk. Animals of all age groups were infected, with a higher molecular prevalence of B. bigemina and A. marginale in young buffalo and calves, respectively, while a stepwise increase in seroprevalence of B. bovis and B. bigemina from calves to adult buffaloes was found. The co-infection by the three pathogens was found in 12% of animals, and when analyzed by pair, the co-infections of B. bovis and B. bigemina, B. bigemina and A. marginale, and B. bovis and A. marginale were found in 20%, 24%, and 26%, respectively, underlying the positive interaction between these pathogens infecting buffaloes. These results provide evidence that tick-borne pathogen infections can be widespread among water buffalo populations in tropical livestock ecosystems. Further studies should evaluate whether these pathogens affect the health status and productive performance of water buffalo and infection risk of these pathogens in cattle cohabiting with buffalo. Univ Agr La Habana, Apartado Postal 18-19, San Jose De Los Lajas 32700, Mayabeque, Cuba Ctr Nacl Sanidad Agr, Apartado Postal 10, San Jose De Las Lajas 32700, Mayabeque, Cuba Univ Paris Est, Ecole Natl Vet Alfort, ANSES, UMR BIPAR,INRA, F-94700 Maisons Alfort, France Univ Fed Rural Rio de Janeiro, Rodovia BR 465,Km 07 S-N, BR-23890000 Seropedica, RJ, Brazil Univ Estadual Paulista, Campus Jaboticabal, BR-14884900 Sao Paulo, Brazil Embrapa Pecuaria Sudeste, Rodovia Washington Luiz,Km 234, BR-13560970 Sao Carlos, SP, Brazil Univ Estadual Paulista, Campus Jaboticabal, BR-14884900 Sao Paulo, Brazil CNPq: CNPq-474648/210-9 FAPESP: 2012/21371-4 CAPES: 089110 National Priority Program for Animal and Plant Health, Ministry of Agriculture, Cuba: MINAGRI-P131LH003007

International audience; Sorghum is a potential substitute for corn/wheat in cereal-based extruded products. Despite agronomic advantages and its rich diversity of phenolic compounds, sorghum kafirins group together and form complex with tannins, leading to a low digestibility. Phenolic content/profile by UPLC-ESI-QTOF-MSE and kafirins polymerization by SE-HPLC were evaluated in wholemeal sorghum extrudates; tannin-rich (#SC319) and tannin-free (#BRS330) genotypes with/without turmeric powder. Total phenolic, proantocyanidin and flavonoid contents were strongly correlated with antioxidant capacity (r > 0.9, p < 0.05). Extrusion increased free (+60%) and decreased bound phenolics (−40%) in #SC319, but reduced both (−40%; −90%, respectively) in #BRS330, which presented lower abundance after extrusion. Turmeric addition did not significantly impact antioxidant activity, phenolic content and profile and kafirins profile. Tannins presence/absence impacted phenolic profiles and polymerization of kafirins which appears related to the thermoplastic process. The extrusion improved proteins solubility and can positively enhance their digestibility (phenolic compounds-proteins interactions), making more accessible to proteolysis in sorghum extrudates.

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International audience

International audience; Background Bemisia tabaci(Hemiptera: Aleyrodidae) represents one of the greatest threats to agricultural crops. Chemical control is the primary tool used in integrated pest management (IPM) programs. However, release of the predatorNesidiocoris tenuis(Hemiptera: Miridae) on tomato plants is a highly recommended control tactic. The objective of this study was to evaluate the efficacy of a commercial borax plus citrus oil (BCO) product againstB. tabaciin the presence and absence ofN. tenuis. The synthetic insecticide lambda-cyhalothrin was used as a positive control. We also evaluated the sublethal effects of BCO on the behavior and predation rate ofN. tenuis. Results Our results demonstrated that BCO, alone and at its maximum recommended field rate forB. tabaci, was not effective in controlling the pest under laboratory conditions. Application of BCO simultaneous withN. tenuisrelease did not reduce the increase in theB. tabacipopulation. Effective control ofB. tabaciwas achieved using onlyN. tenuis. However, synthetic lambda-cyhalothrin pyrethroid, used here as a control, caused high pest mortality and led to on-site extinction ofN. tenuis, which did not occur for insects exposed to BCO. Lambda-cyhalothrin and BCO significantly affected the foraging behavior ofN. tenuis, reducing the predation rate, especially following exposure to lambda-cyhalothrin. Conclusion The insecticide lambda-cyhalothrin achieved satisfactory results in suppressingB. tabaci, but was harmful toN. tenuis. Additionally, lambda-cyhalothrin and BCO affected predator behavior.

For many years, it was believed that only amino acids, dipeptides, and tripeptides could be absorbed and thus reach the bloodstream. Nowadays, the bioavailability of oligopeptides is also considered possible, leading to new research. This pilot study investigates the activity of brush border enzymes on undigested whey protein hydrolysate (WPH) and on simulated intestinal digested (ID) whey hydrolysate and the subsequent absorption of resultant peptides through the proximal jejunum of a 7-week old piglet setup in an Ussing chamber model. Amongst all samples taken, 884 oligopeptides were identified. The brush border peptidase activity was intense in the first 10 min of the experiment, producing several new peptides in the apical compartment. With respect to the ID substrate, 286 peptides were detected in the basolateral compartment after 120 min of enzyme activity, originating from &beta, lactoglobulin (60%) and &beta, casein (20%). Nevertheless, only 0.6 to 3.35% of any specific peptide could pass through the epithelial barrier and thus reach the basolateral compartment. This study demonstrates transepithelial jejunum absorption of whey oligopeptides in an ex vivo model. It also confirmed the proteolytic activity of brush border enzymes on these oligopeptides, giving birth to a myriad of new bioactive peptides available for absorption.

Delineating species and epidemic lineages in fungal plant pathogens is critical to our understanding of disease emergence and the structure of fungal biodiversity, and also informs international regulatory decisions.Pyricularia oryzae (syn. Magnaporthe oryzae)is a multi-host pathogen that infects multiple grasses and cereals, is responsible for the most damaging rice disease (rice blast), and of growing concern due to the recent introduction of wheat blast to Bangladesh from South America. However, the genetic structure and evolutionary history ofM. oryzae, including the possible existence of cryptic phylogenetic species, remain poorly defined. Here, we use whole-genome sequence information for76 M. oryzaeisolates sampled from 12 grass and cereal genera to infer the population structure ofM. oryzae, and to reassess the species status of wheat-infecting populations of the fungus. Species recognition based on genealogical concordance, using published data or extracting previously-used loci from genome assemblies, failed to confirm a prior assignment of wheat blast isolates to a new species (Pyricularia graminis tritici). Inference of population subdivisions revealed multiple divergent lineages withinM. oryzae, each preferentially associated with one host genus, suggesting incipient speciation following host shift or host range expansion. Analyses of gene flow, taking into account the possibility of incomplete lineage sorting, revealed that genetic exchanges have contributed to the makeup of multiple lineages withinM. oryzae. These findings provide greater understanding of the eco-evolutionary factors that underlie the diversification ofM. oryzaeand highlight the practicality of genomic data for epidemiological surveillance in this important multi-host pathogen.ImportanceInfection of novel hosts is a major route for disease emergence by pathogenic micro-organisms. Understanding the evolutionary history of multi-host pathogens is therefore important to better predict the likely spread and emergence of new diseases.Magnaporthe oryzaeis a multi-host fungus that causes serious cereal diseases, including the devastating rice blast disease, and wheat blast, a cause of growing concern due to its recent spread from South America to Asia. Using whole genome analysis of 76 fungal strains from different hosts, we have documented the divergence ofM. oryzaeinto numerous lineages, each infecting a limited number of host species. Our analyses provide evidence that inter-lineage gene flow has contributed to the genetic makeup of multipleM. oryzaelineages within the same species. Plant health surveillance is therefore warranted to safeguard against disease emergence in regions where multiple lineages of the fungus are in contact with one another.

International audience; Climate change adaptation, mitigation and food security may be addressed at the same time by enhancing soil organic carbon (SOC) sequestration through environmentally sound land management practices. This is promoted by the “4 per 1000” Initiative, a multi-stakeholder platform aiming at increasing SOC storage through sustainable practices. The scientific and technical committee of the Initiative is working to identify indicators, research priorities and region-specific practices needed for their implementation. The Initiative received its name due to the global importance of soils for climate change, which can be illustrated by a thought experiment showing that an annual growth rate of only 0.4% of the standing global SOC stocks would have the potential to counterbalance the current increase in atmospheric CO2. However, there are numerous barriers to the rise in SOC stocks and while SOC sequestration can contribute to partly offsetting greenhouse gas emissions, its main benefits are related to increased soil quality and climate change adaptation. The Initiative provides a collaborative platform for policy makers, practitioners, scientists and stakeholders to engage in finding solutions. Criticism of the Initiative has been related to the poor definition of its numerical target, which was not understood as an aspirational goal. The objective of this paper is to present the aims of the initiative, to discuss critical issues and to present challenges for its implementation. We identify barriers, risks and trade-offs and advocate for collaboration between multiple parties in order to stimulate innovation and to initiate the transition of agricultural systems toward sustainability.

International audience; The expansion of agribusiness in all Brazilians regions challenges the future of traditional agricultural systems. This article intends to identify the processes by which traditional farmers maintain agricultural diversity at the soybean frontier in Brazil. The data were obtained from the survey and mapping of agricultural practices and agrobiodiversity with 113 farmers from three indigenous, quilombola and peasant territories of the South, North-East and North of the country. Agricultural diversity in the interstices of soybean plantations (between 66 and 188 crop species and varieties) results from the continuous production of knowledge in experimentation spaces constituted by swidden agriculture. Traditional agricultural knowledge molds a heterogeneous soybean frontier, where the interstices cultivated by communities reveal themselves as islands of agrobiodiversity in a sea of monocultures. Far from being opposed to modernity or the market economy, traditional agricultural knowledge consists of processes of innovation that lie in the ingenious combination of "old" and "modern" practices and varieties. Thus, the concept of dynamic conservation allows to go beyond the common idea of the substitution of local varieties or the erosion of traditional knowledge in the face of agribusiness expansion. On the other hand, even in relatively stabilized traditional territories, the dynamic conservation of agrobiodiversity is threatened by the environmental impacts of soy expansion. Even if traditional ways of practicing agriculture are still operative in the interstices of soybeans, an extra-territorial process of disqualification of local agricultural knowledge underpin these agricultural systems because of the acceleration of rhythms and scales of environmental changes. Thus, measures to recognize, protect and monitor traditional territories are basic conditions for farmers to continue to conserve agrobiodiversity dynamically.; L'expansion de l'agriculture industrielle dans toutes les régions brésiliennes constitue un défi pour l'avenir des systèmes agricoles traditionnels. Cet article vise à identifier les processus par lesquels les agriculteurs traditionnels maintiennent la diversité agricole à la frontière du soja au Brésil. Les données ont été obtenues à partir d'enquêtes et de la cartographie des pratiques agricoles et de l'agrobiodiversité avec 113 agriculteurs amérindiens, quilombolas et paysans sur leurs territoires respectifs dans le Sud, Nord et Nord-Est du pays. La diversité agricole dans les interstices du soja (de 66 à 188 espèces et variétés cultivées dans les différents territoires) résulte de la production continue de connaissances dans des espaces issus de l'agriculture sur brûlis. Les connaissances agricoles traditionnelles modèlent une frontière hétérogène, où les interstices cultivés consituent des îlots d'agrobiodiversité dans une mer de monocultures. Loin de s'opposer à la modernité ou à l'économie de marché, les connaissances agricoles traditionnelles consistent en des processus d'innovation reposant sur la combinaison ingénieuse entre pratiques et de variétés "anciennes" et "modernes". Ainsi, le concept de conservation dynamique permet d'aller au-delà de l'idée de substitution des variétés locales ou de l'érosion des connaissances traditionnelles face à l’avancée de l’agribusiness. Cependant, même dans des territoires traditionnels relativement stabilisés, la conservation dynamique de la biodiversité agricole est menacée par les impacts environnementaux de l'expansion du soja. Si les formes traditionnelles de pratiquer de l’agriculture sont toujours actives dans ces interstices, un processus extraterritorial de disqualification opère toutefois en raison de l’accélération du rythme et de l'ampleur des changements environnementaux. Ainsi, les mesures de reconnaissance, de protection et de surveillance des territoires traditionnels sont les conditions de base pour que les agriculteurs continuent à conserver la biodiversité agricole de manière dynamique.; A expansão do agronegócio em todas as regiões do Brasil desafia o futuro dos sistemas agrícolas tradicionais. Este artigo pretende identificar os processos pelos quais agricultores tradicionais mantêm a diversidade agrícola na fronteira da soja no Brasil. Os dados foram obtidos a partir do levantamento e mapeamento das práticas agrícolas e da agrobiodiversidade junto a 113 agricultores indígenas, quilombolas e camponeses em seus respectivos territórios do Sul, Norte e Nordeste do país. A diversidade agrícola nos interstícios da soja (entre 66 e 188 espécies e variedades cultivadas) resulta da produção contínua de conhecimentos nos espaços oriundos da agricultura de corte e queima. Os conhecimentos agrícolas tradicionais configuram uma fronteira heterogênea, onde os interstícios cultivados por comunidades revelam-se como ilhas de agrobiodiversidade em um mar de monoculturas. Longe de serem opostos à modernidade ou à economia de mercado, os conhecimentos agrícolas tradicionais consistem em processos de inovação que residem na combinação engenhosa entre práticas e variedades "antigas" e "modernas". Assim, o conceito de conservação dinâmica permite ir além da ideia comum da substituição de variedades locais por cultivares comerciais, ou da "erosão" dos conhecimentos tradicionais frente ao avanço do agronegócio. Por outro lado, mesmo em territórios tradicionais relativamente estabilizados, a conservação dinâmica da agrobiodiversidade é ameaçada pelos impactos ambientais da expansão da soja. Por mais que as formas tradicionais de praticar a agricultura sejam ainda operantes nestes interstícios, um processo extra-territorial de desqualificação dos conhecimentos agrícolas locais ameaça os sistemas agrícolas tradicionais, por causa da aceleração dos ritmos e escalas de mudanças ambientais. Assim, medidas de reconhecimento, proteção e monitoramento dos territórios tradicionais são condições básicas para que a(o)s agricultora(e)s sigam conservando a agrobiodiversidade de forma dinâmica.

International audience; Theobroma grandiflorum (Willd. ex Spreng.) Schum. is a tree originating in the Amazon forest. In Brazil, it is known as cupuassu and, like Theobroma cacao, belongs to the family of the Malvaceae. The pulp is used by the food industry and the seeds, which are rich in fatty acids, are used in cosmetics. As for cacao, cupuassu cultivation is affected by the witches' broom disease (WBD), caused by Moniliophthora perniciosa (M. perniciosa). Despite its economical value, cupuassu culture lacks genetic information, compromising its plant breeding program development. The aim of this research was to increase molecular knowledge about WBD resistance. The progeny of 168 individuals obtained by crossing two contrasting cupuassu clones (174 and 1074, resistant and susceptible to WBD, respectively) were evaluated. The first consensus genetic map consisting of 1438 markers was produced using genotyping by sequencing (GBS) and genome sequencing of the neighboring species T. cacao (Criollo B97) as reference. The analysis of synteny between T. cacao and T. grandiflorum showed that the average homology between the linkage groups of the two species was 97.2%. A resistance quantitative trait locus (QTL) was identified on chromosome 6 of resistant parent 174 at marker 6M1252980. The phenotypic data associated with that QTL corresponded to observations after natural and artificial infection with M. perniciosa. The biological process associated with this QTL may play a role in resistance and susceptibility to M. perniciosa.

International audience; The cosmetic and fragrance industry largely exploits citrus essential oils (EOs) because of their aromatic properties. EO compositions are complex and differ between fruit pericarp (PEO) and leaf (LEO). Citrus fruit grow in many countries under very different climates. Seventeen citrus cultivars were selected and their similarities between the two collections were verified by SSR (Single Sequence Repeat) and InDel (Insertion and Deletion) markers to assess the effects of the environment and cultivation practices on the EO yield and composition. LEOs and PEOs were extracted by water distillation and analyzed by GC-MS. PEO yields were generally higher in Corsica than in Bahia, especially in the citron family. PEOs in this family were richer in limonene in Bahia than in Corsica while, conversely, neral, geranial and derivatives were present in a higher proportion in Corsican varieties. A few minor components were site-specific, such as nookaton, a pummelo-specific compound that was not present in grapefruit cultivated in Bahia. If climate change over the last 20 years has not affected the PEO composition in Corsica, the contrasted environmental conditions and cultural practices between Bahia and Corsica could possibly explain the EO variations.

International audience; The expansion of agribusiness in all Brazilians regions challenges the future of traditional agricultural systems. This article intends to identify the processes by which traditional farmers maintain agricultural diversity at the soybean frontier in Brazil. The data were obtained from the survey and mapping of agricultural practices and agrobiodiversity with 113 farmers from three indigenous, quilombola and peasant territories of the South, North-East and North of the country. Agricultural diversity in the interstices of soybean plantations (between 66 and 188 crop species and varieties) results from the continuous production of knowledge in experimentation spaces constituted by swidden agriculture. Traditional agricultural knowledge molds a heterogeneous soybean frontier, where the interstices cultivated by communities reveal themselves as islands of agrobiodiversity in a sea of monocultures. Far from being opposed to modernity or the market economy, traditional agricultural knowledge consists of processes of innovation that lie in the ingenious combination of "old" and "modern" practices and varieties. Thus, the concept of dynamic conservation allows to go beyond the common idea of the substitution of local varieties or the erosion of traditional knowledge in the face of agribusiness expansion. On the other hand, even in relatively stabilized traditional territories, the dynamic conservation of agrobiodiversity is threatened by the environmental impacts of soy expansion. Even if traditional ways of practicing agriculture are still operative in the interstices of soybeans, an extra-territorial process of disqualification of local agricultural knowledge underpin these agricultural systems because of the acceleration of rhythms and scales of environmental changes. Thus, measures to recognize, protect and monitor traditional territories are basic conditions for farmers to continue to conserve agrobiodiversity dynamically.; L'expansion de l'agriculture industrielle dans toutes les régions brésiliennes constitue un défi pour l'avenir des systèmes agricoles traditionnels. Cet article vise à identifier les processus par lesquels les agriculteurs traditionnels maintiennent la diversité agricole à la frontière du soja au Brésil. Les données ont été obtenues à partir d'enquêtes et de la cartographie des pratiques agricoles et de l'agrobiodiversité avec 113 agriculteurs amérindiens, quilombolas et paysans sur leurs territoires respectifs dans le Sud, Nord et Nord-Est du pays. La diversité agricole dans les interstices du soja (de 66 à 188 espèces et variétés cultivées dans les différents territoires) résulte de la production continue de connaissances dans des espaces issus de l'agriculture sur brûlis. Les connaissances agricoles traditionnelles modèlent une frontière hétérogène, où les interstices cultivés consituent des îlots d'agrobiodiversité dans une mer de monocultures. Loin de s'opposer à la modernité ou à l'économie de marché, les connaissances agricoles traditionnelles consistent en des processus d'innovation reposant sur la combinaison ingénieuse entre pratiques et de variétés "anciennes" et "modernes". Ainsi, le concept de conservation dynamique permet d'aller au-delà de l'idée de substitution des variétés locales ou de l'érosion des connaissances traditionnelles face à l’avancée de l’agribusiness. Cependant, même dans des territoires traditionnels relativement stabilisés, la conservation dynamique de la biodiversité agricole est menacée par les impacts environnementaux de l'expansion du soja. Si les formes traditionnelles de pratiquer de l’agriculture sont toujours actives dans ces interstices, un processus extraterritorial de disqualification opère toutefois en raison de l’accélération du rythme et de l'ampleur des changements environnementaux. Ainsi, les mesures de reconnaissance, de protection et de surveillance des territoires traditionnels sont les conditions de base pour que les agriculteurs continuent à conserver la biodiversité agricole de manière dynamique.; A expansão do agronegócio em todas as regiões do Brasil desafia o futuro dos sistemas agrícolas tradicionais. Este artigo pretende identificar os processos pelos quais agricultores tradicionais mantêm a diversidade agrícola na fronteira da soja no Brasil. Os dados foram obtidos a partir do levantamento e mapeamento das práticas agrícolas e da agrobiodiversidade junto a 113 agricultores indígenas, quilombolas e camponeses em seus respectivos territórios do Sul, Norte e Nordeste do país. A diversidade agrícola nos interstícios da soja (entre 66 e 188 espécies e variedades cultivadas) resulta da produção contínua de conhecimentos nos espaços oriundos da agricultura de corte e queima. Os conhecimentos agrícolas tradicionais configuram uma fronteira heterogênea, onde os interstícios cultivados por comunidades revelam-se como ilhas de agrobiodiversidade em um mar de monoculturas. Longe de serem opostos à modernidade ou à economia de mercado, os conhecimentos agrícolas tradicionais consistem em processos de inovação que residem na combinação engenhosa entre práticas e variedades "antigas" e "modernas". Assim, o conceito de conservação dinâmica permite ir além da ideia comum da substituição de variedades locais por cultivares comerciais, ou da "erosão" dos conhecimentos tradicionais frente ao avanço do agronegócio. Por outro lado, mesmo em territórios tradicionais relativamente estabilizados, a conservação dinâmica da agrobiodiversidade é ameaçada pelos impactos ambientais da expansão da soja. Por mais que as formas tradicionais de praticar a agricultura sejam ainda operantes nestes interstícios, um processo extra-territorial de desqualificação dos conhecimentos agrícolas locais ameaça os sistemas agrícolas tradicionais, por causa da aceleração dos ritmos e escalas de mudanças ambientais. Assim, medidas de reconhecimento, proteção e monitoramento dos territórios tradicionais são condições básicas para que a(o)s agricultora(e)s sigam conservando a agrobiodiversidade de forma dinâmica.

International audience; A root-knot nematode parasitizing rice (Oryza sativa L.) in Santa Catarina state (Brazil) was identified as Meloidogyne oryzae Maas, Sanders and Dede, 1978 using different approaches. The specimens studied from this Brazilian population were compared with the type description of M. oryzae from Suriname, with additional morphological, biochemical and molecular characterization. The female has a longer stylet (15.0 μm) when compared with M. graminicola (11.2 μm) with irregularly shaped knobs, vulva offset and slightly protruding in posterior region. The lip region was distinct from first body annuli, and labial disc and the medial lips form an anchor-shaped structure. Perineal patterns were similar to M. graminicola. The male has a lip region offset and the presence of few short and irregular lines; medial lips divided, not fused with labial disc and stylet (18.2 μm) longer than in M. graminicola (16.8 μm). Second-stage juvenile (J2) tail (75.8 μm) was longer than in M. graminicola (70.9 μm) with a very long narrow hyaline portion (22 μm in M. oryzae and 17.9 μm in M. graminicola). Biochemically, it presented a distinct esterase profile (Est O1=R1), differentiating it from M. graminicola (Est VS1). The number of chromosomes was 3n = 50–56, and in DNA sequences of ITS1–5.8S–ITS2 rRNA the two populations of M. oryzae clustered together with other mitotic parthenogenetic species, differentiating them from M. graminicola with n = 18 chromosomes and clustered with meiotic species. Phylogenetic analysis using neutral markers (AFLP and RAPD) showed that both M. oryzae populations form a coherent, closely related cluster separately from M. graminicola isolates. This study represented the first detection of M. oryzae in Brazil and the second in the world after the species description in 1971.

International audience; The cupuassu tree (Theobroma grandiflorwn) is a crop of great economic importance to Brazil, mainly for its pulp and seeds, which are used in food industry. However, cupuassu fruit production is threatened by witches' broom disease caused by the fungus Moniliophthora perniciosa. As elements of its defense mechanisms, the plant can produce and accumulate pathogenesis-related (PR) proteins such as chitinases and osmotins. Here, we identified three cupuassu PR proteins (TgPR3, TgPR5 and TgPR8) from cupuassu-M. perniciosa interaction RNA-seq data. TgPR3 and TgPR8 corresponded to chitinases, and TgPR5 to osmotin; they are phylogenetically related to cacao and to Arabidopsis PR sequences involved in biotic and abiotic stress. The TgPR proteins' tridimensional structure was obtained through homology modeling, and molecular docking with chitin and chitosan showed that the TgPR proteins can interact with both cell wall molecules and presented a higher affinity for chitosan. TgPR gene expression was analyzed by RT-qPCR on resistant and susceptible cupuassu genotypes infected by M. perniciosa at 8, 24, 48 and 72 h after infection (hai). The TgPR genes showed higher expression in resistant plants compared to the susceptible ones, mainly for TgPR5 at 8 and 24 hai, while the expression was lower in the susceptible cupuassu plants. To our knowledge, this is the first in silico and in vitro reports of cupuassu PR protein. The data suggested that TgPRs could be involved in recognizing mechanisms of the plant's innate immune system through chitin receptors. Our results also suggest a putative role of chitinase/chitosanase for the TgPR5/osmotin.

Several Avian paramyxoviruses 1 (synonymous with Newcastle disease virus or NDV, used hereafter) classification systems have been proposed for strain identification and differentiation. These systems pioneered classification efforts; however, they were based on different approaches and lacked objective criteria for the differentiation of isolates. These differences have created discrepancies among systems, rendering discussions and comparisons across studies difficult. Although a system that used objective classification criteria was proposed by Diel and co-workers in 2012, the ample worldwide circulation and constant evolution of NDV, and utilization of only some of the criteria, led to identical naming and/or incorrect assigning of new sub/genotypes. To address these issues, an international consortium of experts was convened to undertake in-depth analyses of NDV genetic diversity. This consortium generated curated, up-to-date, complete fusion gene class I and class II datasets of all known NDV for public use, performed comprehensive phylogenetic neighbor-Joining, maximum-likelihood, Bayesian and nucleotide distance analyses, and compared these inference methods. An updated NDV classification and nomenclature system that incorporates phylogenetic topology, genetic distances, branch support, and epidemiological independence was developed. This new consensus system maintains two NDV classes and existing genotypes, identifies three new class II genotypes, and reduces the number of sub-genotypes. In order to track the ancestry of viruses, a dichotomous naming system for designating sub-genotypes was introduced. In addition, a pilot dataset and sub-trees rooting guidelines for rapid preliminary genotype identification of new isolates are provided. Guidelines for sequence dataset curation and phylogenetic inference, and a detailed comparison between the updated and previous systems are included. To increase the speed of phylogenetic inference and ensure consistency between laboratories, detailed guidelines for the use of a supercomputer are also provided. The proposed unified classification system will facilitate future studies of NDV evolution and epidemiology, and comparison of results obtained across the world., Highlights • An international consortium phylogenetically studied the diversity of NDV. • Consensus objective NDV classification and nomenclature system was developed. • Optimal phylogenetic inference method with guidelines is recommended. • Curated, up-to-date, complete fusion gene datasets for public use were created. • Three new NDV genotypes were identified.

Since the early 2000s conservation agriculture (CA) has been promoted in the Lake Alaotra region of Madagascar for a more sustainable and profitable agriculture. There is, however, little known about its performance in low-input rainfed rice-based cropping systems. We conducted a study during two growing seasons (2013/14 and 2014/15) on an experiment that was established in 2009 at the agricultural research station of the National Center for Applied Research and Rural Development (FOFIFA) in the Lake Alaotra region of Madagascar. The experimental setup was a randomized block design with four replications. Two soil/residue management treatments were studied, conventional tillage without residue retention (CT) and no-tillage with residue retention (NT). These two treatments were tested for a 2-year rotation of maize + Dolichos lablab followed by rice (MD//R) and a 3-year rotation of maize + Stylosanthes guianensis, followed by S. guianensis in the second year, and rice in the third year (MS//S//R). During the 2013/14 and 2014/15 seasons, two levels of weed pressure: 'high' and 'low' were introduced as a split-plot design on the rice plots. The main determining factors of rice yield in the study region were studied: radiation interception, weed infestation, soil moisture and soil mineral nitrogen (N). Our results showed that five to six years of continuous practice of NT with retention of high amounts of crop residues (more than 5 Mg DM ha−1) on the soil surface had a significant (p = 0.02) positive effect on rice yield, irrespective of the level of weed pressure and type of crop rotation. CA systems significantly (p

International audience; The aim of this work was to study the regulation of coffee DREB-like genes in leaves of C. arabica subjected to cold, heat, low relative humidity, exogenous abscisic acid and high light stress, as well as in leaves and roots of drought-tolerant and drought-susceptible clones of Coffea canephora subjected to water limitation. In C. arabica, CaERF017 was the most expressed gene under low temperatures and relative humidity, while low humidity and high temperatures up-regulated the expression of CaERF053 and CaERF014, respectively. Under water limitation, CcDREB1B, CcRAP2.4, CcERF027, CcDREB1D and CcTINY were the most expressed genes mainly in leaves of drought-tolerant C. canephora. On the other hand, expression of the CcERF016, CcRAP2.4 and CcDREB2F genes was highly up-regulated under water limitation in the roots of drought-susceptible C. canephora clone 22. We previously reported fine-tuned regulation of CcDREB1D promoter haplotypes (HP15, HP16 and HP17) in transgenic C. arabica subjected to low humidity. Here, we investigated the regulation of these haplotypes under high light, cold, heat, and abscisic acid (ABA) stress. In apical buds and leaf guard cells, GUS-stained percentages were higher in pHP16L-transformed plants subjected to low humidity, high light and ABA stress than in pHP17L- and pHP15L-transformed plants. We also reported up-regulated expression of the endogenous CaDREB1D gene for both the cold and low humidity in leaves of pHP16L-transformed C. arabica suggesting a key role of this gene in controlling the responses of coffee plants to abiotic stress probably through an ABA-dependent pathway.

Drought episodes decrease plant growth and productivity, which in turn cause high economic losses. Plants naturally sense and respond to water stress by activating specific signalling pathways leading to physiological and developmental adaptations. Genetically engineering genes that belong to these pathways might improve the drought tolerance of plants. The abscisic acid (ABA)-responsive element binding protein 1/ABRE binding factor (AREB1/ABF2) is a key positive regulator of the drought stress response. We investigated whether the CRISPR activation (CRISPRa) system that targets AREB1 might contribute to improve drought stress tolerance in Arabidopsis. Arabidopsis histone acetyltransferase 1 (AtHAT1) promotes gene expression activation by switching chromatin to a relaxed state. Stable transgenic plants expressing chimeric dCas9HAT were first generated. Then, we showed that the CRISPRa dCas9HAT mechanism increased the promoter activity controlling the β-glucuronidase (GUS) reporter gene. To activate the endogenous promoter of AREB1, the CRISPRa dCas9HAT system was set up, and resultant plants showed a dwarf phenotype. Our qRT-PCR experiments indicated that both AREB1 and RD29A, a gene positively regulated by AREB1, exhibited higher gene expression than the control plants. The plants generated here showed higher chlorophyll content and faster stomatal aperture under water deficit, in addition to a better survival rate after drought stress. Altogether, we report that CRISPRa dCas9HAT is a valuable biotechnological tool to improve drought stress tolerance through the positive regulation of AREB1.

International audience; Following many decades of work on the taxonomy, biology and ecology of the globally-distributed tropical earthworm Pontoscolex corethrurus (Muller, 1857), morphological and molecular data have shown that the stability and effectiveness of nomenclature depends on the designation of a neotype from the type locality. We do that, with all the required justifications, and provide sufficient information to permit the correct identification of this species.

International audience; Abscisic acid (ABA) is an essential phytohormone that regulates growth, development and adaptation of plants to environmental stresses. In Arabidopsis and other higher plants, ABA signal transduction involves three core components namely PYR/PYL/RCAR ABA receptors (PYLs), type 2C protein phosphatases (PP2Cs) and class III SNF-1-related protein kinase 2 (SnRK2s). In the present study, we reported the identification and characterization of the core ABA signaling components in Setaria viridis, an emerging model plant for cereals and feedstock crops presenting C4 metabolism, leading to the identification of eight PYL (SvPYL1 to 8), twelve PP2C (SvPP2C1 to 12) and eleven SnRK2 (SvSnRK2.1 through SvSnRK2.11) genes. In order to study the expression profiles of these genes, two different S. viridis accessions (A10.1 and Ast-1) were submitted to drought, salinity and cold stresses, in addition to application of exogenous ABA. Differential gene expression profiles were observed in each treatment and plant genotype, demonstrating variations of ABA stress responses within the same species. These differential responses to stresses were also assessed by physiological measurements such as photosynthesis, stomatal conductance and transpiration rate. This study allows a detailed analysis of gene expression of the core ABA signaling components in Setaria viridis submitted to different treatments and provides suitable targets for genetic engineering of C4 plants aiming tolerance to abiotic stresses.

The root-knot nematode (RKN) Meloidogyne incognita is the main nematode causing losses to the cotton crop in Brazil. In order to implement control strategies within integrated management, an accurate identification of the nematode populations prevailing in the cotton production areas is necessary. This study aimed to assess the genetic variability and aggressiveness of RKN populations from cotton production areas in Bahia state, Brazil. All populations were characterized biochemically and molecularly and identified as M. incognita. RAPD and AFLP markers detected 44% of polymorphic fragments among the 13 populations of this species. The 10 M. incognita populations collected in Bahia presented 33.7% of diversity when compared to each other, and 25% when the population from Barreiras (the most polymorphic) was excluded. This polymorphism increased when populations from other Brazilian states were included. The aggressiveness and virulence among populations from Bahia towards different cotton accessions (susceptible/resistant) was also studied. None of the populations showed virulence against the moderately resistant (Clevewilt 6, Wild Mexican Jack Jones and LA 887) and highly resistant (CIR1348 and M-315 RNR) cultivars. Two M. incognita populations from Barreiras were the most aggressive, reaching reproduction factors of 539 and 218, respectively, in the susceptible cultivar FiberMax 966. The most aggressive population (8) was also the most genetically divergent in phylogenetic analyses. These results demonstrate that diversity of M. incognita populations from cotton farms in Bahia is not related to virulence against resistant accessions, which suggests that cultivars containing one or two resistance genes with good agronomic characteristics could be used in infested commercial areas in Bahia state, Brazil. Made available in DSpace on 2020-01-14T00:41:50Z (GMT). No. of bitstreams: 1 Diversityofmeloidogyneincognita.pdf: 477080 bytes, checksum: 4aca51ad941dc17bc82bc44a60bcc0d6 (MD5) Previous issue date: 2019

International audience; The upland rice (UR) crop system located in the Brazilian savannas (states of Mato Grosso, Rondonia, Tocantins and Goias) is the main upland rice growing area of Brazil and the largest rainfed rice growing area in Latin America. It plays an important social and economic role in central Brazil. UR cropped area, however, has decreased by 70% in the last two decades, partly due to high drought risk. Here, we hypothesize that the UR breeding program's focus on direct grain selection for wide adaptation has led to an increase in yield potential but a reduction in the capacity of modem cultivars to maintain yield under drought stress. Using the ORYZAv3 rice crop model, we analyzed changes in relative and absolute drought impact for cultivars representative of three decades of breeding: 1980s (1986-1992), 1990s (1993-2002), and 2000s (2003-2013). We found a mean increase in relative drought impact of 12% (0.35% per year) between 1980s and 2000s. Most of the increase occurred during 1980s and 1990s (7%), where a major shift from landraces (i.e. Douradao) to modem cultivars (i.e. cv. BRS Primavera) occurred in the breeding program. Drought adaptation traits such as greater root length density, shorter cycle, and lower stomatal sensitivity to drought have been systematically bred out of the UR material in the period 1980-2013. We recommend the UR breeding program to be adjusted by better targeting to specific drought environments, and by taking into account drought stress profiles and environmental co-variables in statistical analyses for genotype selection. Moreover, physiological studies on tradeoffs between yield potential and drought tolerance should be performed for each target environment to dissect plant traits that confer both high yield potential and low drought sensitivity. These strategies will ultimately ensure that newly released cultivars are adapted to the environmental conditions of the study region, therefore reducing agroclimatic risk for UR farmers.

Chilling requirement (CR) for bud dormancy completion determines the time of bud break in apple (Malus × domestica Borkh.). The molecular control of bud dormancy is highly heritable, suggesting a strong genetic control of the trait. An available Infinium II SNP platform for genotyping containing 8,788 single nucleotide polymorphic markers was employed, and linkage maps were constructed in a F1 cross from the low CR M13/91 and the moderate CR cv. Fred Hough. These maps were used to identify quantitative trait loci (QTL) for bud break date as a trait related to dormancy release. A major QTL for bud break was detected at the beginning of linkage group 9 (LG9). This QTL remained stable during seven seasons in two different growing sites. To increase mapping efficiency in detecting contributing genes underlying this QTL, 182 additional SNP markers located at the locus for bud break were used. Combining linkage mapping and structural characterization of the region, the high proportion of the phenotypic variance in the trait explained by the QTL is related to the coincident positioning of Arabidopsis orthologs for ICE1, FLC, and PRE1 protein-coding genes. The proximity of these genes from the most explanatory markers of this QTL for bud break suggests potential genetic additive effects, reinforcing the hypothesis of inter-dependent mechanisms controlling dormancy induction and release in apple trees. Made available in DSpace on 2019-06-12T00:39:12Z (GMT). No. of bitstreams: 1 fpls1000033.pdf: 2246583 bytes, checksum: 39a0aa3363675b7338cebcaa1d270aee (MD5) Previous issue date: 2019

International audience; Phenological asynchrony between fruit crops and pests consists of a discrepancy between the period of fruit susceptibility and that of high pest abundance in the orchards. Therefore, it may be used for reducing pesticide applications. We assayed the potential phenological asynchrony between peach cultivars with different growing cycles and the Anastrepha fraterculus (Diptera: Tephritidae). To this end, we assessed fruit infestation by A. fraterculus at harvest for one growing season (2012-2013) in early, average and late maturing peach cultivars. Moreover, the fruit infestation was checked for non-cultivated native and non-cultivated wild exotic plant hosts around the peach orchards of the experimental area during 2013 and 2014. In addition, we monitored A. fraterculus abundance weekly during three consecutive growing seasons, S1 (2011-2012), S2 (2012-2013) and S3 (2013-2014), to assess phenological asynchrony between peach cultivars and A. fraterculus. In particular, we checked the influence of meteorological variables on A. fraterculus abundance, and tested if A. fraterculus abundance at the time when fruits are susceptible differed among cultivars. Eventually we discuss the possibility of sustainable management of peach in southern Brazil. This study constitutes a first assessment of the periods of crop vulnerability and pest presence in peach orchards in South of Brazil and provides necessary information for taking advantage of the phenological asynchrony phenomenon for this pest-crop association.

International audience; Plant dehydrins (DNHs) belong to the LEA (Late Embryogenesis Abundant) protein family and are involved in responses to multiple abiotic stresses. DHNs are classified into five subclasses according to the organization of three conserved motifs (K-; Y-; and S-segments). In the present study, the DHN protein family was characterized by molecular phylogeny, exon/intron organization, protein structure, and tissue-specificity expression in eight Fabaceae species. We identified 20 DHN genes, encompassing three (YnSKn, SKn, and K-n) subclasses sharing similar gene organization and protein structure. Two additional low conserved DHN Phi-segments specific to the legume SKn-type of proteins were also found. The in silico expression patterns of DHN genes in four legume species (Arachis duranensis, A. ipaensis, Glycine max, and Medicago truncatula) revealed that their tissue-specific regulation is associated with the presence or absence of the Y-segment. Indeed, DHN genes containing a Y-segment are mainly expressed in seeds, whereas those without the Y-segment are ubiquitously expressed. Further qRT-PCR analysis revealed that, amongst stress responsive dehydrins, a SKn-type DHN gene from A. duranensis (AdDHN1) showed opposite response to biotic and abiotic stress with a positive regulation under water deficit and negative regulation upon nematode infection. Furthermore, transgenic Arabidopsis lines overexpressing (OE) AdDHN1 displayed improved tolerance to multiple abiotic stresses (freezing and drought) but increased susceptibility to the biotrophic root-knot nematode (RKN) Meloidogyne incognita. This contradictory role of AdDHN1 in responses to abiotic and biotic stresses was further investigated by qRT-PCR analysis of transgenic plants using a set of stress-responsive genes involved in the abscisic acid (ABA) and jasmonic acid (JA) signaling pathways and suggested an involvement of DHN overexpression in these stress-signaling pathways.

International audience; In Africa, peri-urban vegetable production systems supply perishable vegetables to the rapidly expanding urban centers. These highly intensive systems are characterized by high levels of pests and diseases and an excessive use of synthetic pesticides to reduce their population densities. Root-knot nematodes (RKN) are especially prevalent in these systems but are often not recognized, or diagnosed correctly. The limited ability to accurately identify these pathogens likely results in the inappropriate use and misuse of control measures, such as genetic resistance, crop rotation, or synthetic chemicals. Given the perceived importance of RKN, a species characterization study was conducted in pen-urban vegetable (amaranthus, cabbage, pepper, carrot, cassava, eggplant, okra, tomato) fields and some coffee plantations, in Benin, Kenya, Nigeria, Tanzania and Uganda. Meloidogyne spp. were characterized from 143 field samples using esterase phenotypes (EST) and SCAR markers. Five known species were identified: three phenotypes for M. javanica populations (EST J3, Rm: 1.0, 1.25, 1.4; EST J2a, Rm: 1.0, 1.4; EST J2b, Rm: 1.0, 1.25), two for M. incognita (EST Il, Rm: 1.0; EST 12, Rm: 1.05, 1.0), one for M. arenaria (EST A2, Rm: 1.2, 1.3), one for M. enterolobii (EST E4, Rm: 0.70, 0.75, 0.90, 0.95), one for M. izalcoensis (EST 14 Rm: 0.86, 0.96, 1.24, 1.30) and two unusual esterase phenotypes for two unknown species, named Meloidogyne sp.1 and sp.2. Combinations of species were detected from numerous locations. Genetic diversity was further studied using RAPD primers, by comparing a subset of the sampled populations from Africa and some populations from Brazil and El Salvador. The analysis identified separate clusters of the more common and minor species, with low variability observed for African and American populations. The SCAR markers correctly identified all Meloidogyne species with the exception of M. ethiopica, Meloidogyne sp.1 and Meloidogyne sp.2. For Meloidogyne sp.1, the SCAR markers corresponded wrongly to M. javanica and M. arenaria, and for Meloidogyne sp.2 to M. incognita. This demonstrates the shortcomings of using SCAR markers alone, which can generate erroneous results for RKN species. Further morphological and molecular studies are required to clarify the identity of these two atypical species.

Root-knot nematodes (RKN) cause important production losses of rice (Oryza sativa L.) in the world. Together with Meloidogyne graminicola Golden and Birchfield 1965, M. oryzae Maas, Sanders and Dede, 1978 and M. salasi López, 1984 have been causing damages in irrigated rice fields in Central and South America. In addition, six other RKN species may occur in rice fields in other regions of the world. Correct identification of Meloidogyne spp. is difficult but essential for the management of rice RKNs. The objective of this study was to develop some species-specific molecular markers for the diagnosis of South American RKN rice-related species. Isozyme phenotypes indicated the occurrence of some RKN species in the Brazilian samples, namely M. graminicola, M. oryzae, M. javanica, and two cryptic species designated as Meloidogyne sp. 2 and Meloidogyne sp. 3. Random amplified polymorphic DNA (RAPD) analysis of 16 isolates revealed interspecific genetic polymorphism between Meloidogyne spp., but isolates belonging to the same species (i.e., sharing the same esterase phenotype) always clustered together, whatever the species considered. Specific SCAR markers of 230, 120, and 160 bp were developed for M. graminicola, M. oryzae, and M. salasi, respectively. These SCAR markers may be potential molecular tools for application in routine diagnostic procedures subject to their validation with other rice RKN field populations in the world. Made available in DSpace on 2019-01-07T23:50:25Z (GMT). No. of bitstreams: 1 CesarBauerpdis12172015re.pdf: 794039 bytes, checksum: 830120057aef2230c37cfa99698e16ce (MD5) Previous issue date: 2019-01-07

Arbuscular mycorrhizal fungi (AMF) play a major role as biofertilizer for sustainable agriculture. Nevertheless, it is still poorly documented whether inoculated AMF can successfully establish in field soils as exotic AMF and improve plant growth and productivity. Further, the fate of an exogenous inoculum is still poorly understood. Here, we pre-inoculated two cultivars (Tasset and Gola) of the fruit tree Ziziphus mauritiana (jujube) with the exotic AM fungus Rhizophagus irregularis isolate IR27 before transplantation in the field. In two experiments, tracking and quantification of R. irregularis IR27 were assessed in a 13-month-old jujube and an 18-month-old jujube in two fields located in Senegal. Our results showed that the inoculant R. irregularis IR27 was quantitatively traced and discriminated from native R. irregularis isolates in roots by using a qPCR assay targeting a fragment of the RNA polymerase II gene (RPB1), and that the inoculum represented only fractions ranging from 11 to 15% of the Rhizophagus genus in the two plantations 13 and 18 months after transplantation, respectively. This study validates the use of the RPB1 gene as marker for a relative quantification of a mycorrhizal inoculant fungus isolate in the field.

The pathovar viticola of Xanthomonas citri causes bacterial canker of grapevine. This disease was first recorded in India in 1972, and later in Brazil in 1998, where its distribution is currently restricted to the northeastern region. A multilocus sequence analysis (MLSA) based on seven housekeeping genes and a multilocus variable number of tandem repeat analysis (MLVA) with eight loci were performed in order to assess the genetic relatedness among strains from India and Brazil. Strains isolated in India from three related pathovars affecting Vitaceae species and pathogenic strains isolated from Amaranthus sp. found in bacterial canker-infected vineyards in Brazil were also included. MLSA revealed lack of diversity in all seven genes and grouped grapevine and Amaranthus strains in a monophyletic group in X. citri. The VNTR (variable number of tandem repeat) typing scheme conducted on 107 strains detected 101 haplotypes. The total number of alleles per locus ranged from 5 to 12. A minimum spanning tree (MST) showed that Brazilian strains were clearly separated from Indian strains, which showed unique alleles at three loci. The two strains isolated from symptomatic Amaranthus sp. presented unique alleles at two loci. STRUCTURE analyses revealed three groups congruent with MST and a fourth group with strains from India and Brazil. Admixture among populations were observed in all groups. MST, STRUCTURE and e-BURST analyses showed that the strains collected in 1998 belong to two distinct groups, with predicted founder genotypes from two different vineyards in the same region. This suggest that one introduction of grape planting materials contaminated with genetically distinct strains took place, which was followed by pathogen adaptation. Genome sequencing of one Brazilian strain confirmed typical attributes of pathogenic xanthomonads and allowed the design of a complementary VNTR typing cheme dedicated to X. citri pv. viticola that will allow further epidemiological survey of this genetically monomorphic pathovar. Made available in DSpace on 2019-11-29T18:07:54Z (GMT). No. of bitstreams: 1 Xanthomonascitripv.viticolaAffectingGrapevineinBrazil2019.pdf: 3096692 bytes, checksum: ec2b3ffb0c06180736f471cfff22e23f (MD5) Previous issue date: 2019

International audience; Longevity is an important trait due to its relationship with profitability. Type traits have been used as indirect predictors for productive life. The objective of this study was to evaluate the relationship of 20 type traits on length of productive life in Brazilian Holsteins, using a piecewise Weibull proportional hazard model. Three analyses were performed i) productive life was corrected for within herd level of production as a proxy for functional longevity, which included the time-dependent effects of region within year, class of milk production within herdyear, milk production class within lactation number, fat class and protein contents within herd and (variation in) herd size as well as the time-independent fixed effect of age at first catering and the type trait score; ii) the effects related to production were omitted from the first model (true longevity) and iii) with the first model, the effect of type was also studied considering five classes of percentage of type-scored cows within the herd. All analyses were performed using the Survival Kit program. The final score, angularity, top line, udder texture and suspensory ligament showed the strongest relationship with productive life. When type traits were available only for a small fraction of the herd, the cows had a better chance of remaining longer in the herd. The absence of type trait phenotypes was associated with a strong increase of culling risk for the cows. Type traits were not found to be good indirect predictors of productive life in Brazil.

A significant portion of the Cerrado (Brazilian savanna) has been replaced by major crops such as soybean. This may reveal populations of nematodes with different genetic backgrounds compared to cultivated fields. The objectives of this study were to evaluate the genetic variability and aggressiveness of isolates ofMeloidogynespp., contrasting nematodes from preserved areas of the Cerrado with those originating from cultivated soybean fields. Cluster analysis separated isolates ofMeloidogynespp. and isolates from Cerrado and soybean but did not separate an aggressiveMeloidogyne morocciensisisolate. The aggressiveness of six selected populations ofMeloidogynespp. from Cerrado and soybean against soybean cultivars was evaluated. Results showed that populations ofM. javanicaandM. incognitafrom Cerrado and soybean showed similar aggressiveness. However, forM. morocciensis, the population from soybean was much more aggressive than the one from Cerrado. Aggressiveness is a very intriguing subject that needs special attention for future research in nematology.

International audience; Direct seeding mulch-based cropping (DMC) systems are often considered as an efficient way of combining ecological sustainability and economic viability while maintaining or increasing agricultural productivity. This paper describes a modelling analysis of the functioning of family farms in rural settlements of the agrarian reform in the Cerrados of Brazil. The aim was to assess the impact of the introduction of DMC systems with and without cover crops on crop-livestock management and net household income. A bio-economic farm model based on optimization of a utility function under multiple constraints was developed, capturing the interactions between livestock activities and the introduction of DMC systems. The model was run for six farms representing three farm types in the study area: 1) subsistence-oriented mixed crop-livestock farms; 2) market-oriented dairy farms; and 3) mixed crop-livestock farms, oriented to meat marketing. The following maize-based DMC systems were evaluated: a DMC system with mulch from residues of the previous maize crop and no cover crop, and two DMC systems with a fodder species, Brachiaria brizanta or Cajanus cajan, as cover crop. The simulated adoptability of DMC systems by farmers of the assentamentos depended to a large extent on the yields and feed quality of the fodder species. The modelling results suggested that DMC with C cajan as cover crop was the best suitable option for all simulated farm types. This was mainly explained by its high feed value (expressed in crude protein content). Furthermore, in the process of intensification and specialization in dairy production, farmers were likely to shift from using maize for pig husbandry to feeding it to the dairy cows. The introduction of cover crops in the farm systems was a source of additional animal feed during the dry season that was cheaper than the purchase of feed concentrates, when the size of the dairy herd did not exceed a certain threshold.

UMR BFP - Equipe Mollicutes; International audience; When huanglongbing (HLB) was found in Brazil in 2004, 'Candidatus Liberibacter americanus' was infecting most of the trees while 'Ca. L. asiaticus' was present in a minor proportion. Currently, 'Ca. L. asiaticus' is the predominant bacterium associated with HLB in citrus trees in São Paulo (SP) and Minas Gerais (MG) States, the major citrus-growing regions in Brazil. A phytoplasma from the 16SrIX group was associated with HLB symptoms in Brazil in 2007, in plants free of Liberibacter spp. In this report, HLB samples testing negative for 'Ca. L. asiaticus', 'Ca. L. americanus', and 16SrIX phytoplasma were infected with 16SrIII phytoplasmas. Coinfection with 'Ca. L. asiaticus' and 16SrIII was also found. The 16S ribosomal RNA (rRNA) gene sequences from 22 samples were obtained and sequenced, confirming that the 16SrIII group phytoplasma is associated with HLB symptoms in SP and MG States. Ten single-nucleotide polymorphisms (SNPs) were found in the 1,427-bp 16S rRNA gene sequences from 16SrIII phytoplasmas from citrus, whereas none was detected in 16S rRNA gene sequences among 16SrIX phytoplasma from citrus. Ribosomal protein (rp) rpsSrplVrpsC gene sequences were amplified with 16SrIII group-specific primers, sequenced from a subset of nine samples, and assembled into three groups based on eight SNPs. SNPs in 16S rRNA gene and rp gene sequences are common in 16SrIII phytoplasmas from other hosts and this phytoplasma group is widespread in South America. 16SrIII phytoplasmas highly related are commonly found in Melia azedarach, a widespread tree in Brazil and Argentina. The finding of a new phytoplasma associated with HLB symptoms belonging to the 16SrIII group reinforces the need to develop diagnostic tools to assess HLB-associated microbiomes.

International audience; Availability of digital elevation models (DEM) of increased spatial resolution has triggered interest in texture-based methods for automated geomorphometry. This prospect is all the more appealing concerning tropical countries for which mapping of geomorphic entities has remained limited despite its relevance for natural resource assessment and land planning. In this paper we applied to the Shuttle Radar Topography Mission (SRTM) DEM a multiscale texture analysis based on Fourier 2D periodogram (FOTO method) to reach a spatially coherent mapping that would agree with current knowledge over the conterminous territories of French Guiana and Amapa (Brazil). Through a principal component analysis, FOTO-extracted textural features were found complementary and combined with six common physiographic criteria (convexity, wetness index, dissection, elevation, and percent of steep and low slopes) calculated from the DEM. This provided a primary semiautomated mapping of 16 classes of landform types. To increase legibility, we aggregated into eight landscape unit classes that were the most similar in terms of texture and relief criteria while being frequently contiguous. The resulting map was compared with existing maps that were, however, more local or of lesser resolution and informative content over the region of interest. Multiscale Fourier spectra proved useful to depict land surface texture and, in synergy with relief variables, allowed identifying a large variety of landforms for broad-scale geomorphic mapping in the humid tropics.

Background The Root-Knot Nematode (RKN), Meloidogyne arenaria, significantly reduces peanut grain quality and yield worldwide. Whilst the cultivated species has low levels of resistance to RKN and other pests and diseases, peanut wild relatives (Arachis spp.) show rich genetic diversity and harbor high levels of resistance to many pathogens and environmental constraints. Comparative transcriptome analysis can be applied to identify candidate resistance genes. Results Transcriptome analysis during the early stages of RKN infection of two peanut wild relatives, the highly RKN resistant Arachis stenosperma and the moderately susceptible A. duranensis, revealed genes related to plant immunity with contrasting expression profiles. These included genes involved in hormone signaling and secondary metabolites production and also members of the NBS-LRR class of plant disease resistance (R) genes. From 345 NBS-LRRs identified in A.duranensis reference genome, 52 were differentially expressed between inoculated and control samples, with the majority occurring in physical clusters unevenly distributed on eight chromosomes with preferential tandem duplication. The majority of these NBS-LRR genes showed contrasting expression behaviour between A. duranensis and A. stenosperma, particularly at 6 days after nematode inoculation, coinciding with the onset of the Hypersensitive Response in the resistant species. The physical clustering of some of these NBS-LRR genes correlated with their expression patterns in the contrasting genotypes. Four NBS-LRR genes exclusively expressed in A. stenosperma are located within clusters on chromosome Aradu. A09, which harbors a QTL for RKN resistance, suggesting a functional role for their physical arrangement and their potential involvement in this defense response. Conclusion The identification of functional novel R genes in wild Arachis species responsible for triggering effective defense cascades can contribute to the crop genetic improvement and enhance peanut resilience to RKN. Electronic supplementary material The online version of this article (10.1186/s12870-018-1373-7) contains supplementary material, which is available to authorized users.

Brown rot caused by Monilinia spp. provokes dramatic losses of peach in all production regions. In this context, the general objective of our work is to develop sustainable ways to fight against this damaging disease. This study explored phenolic and triterpenoid diversity of fruit skin together with brown rot resistance. A Brazilian peach collection and an interspecific cross between P. davidiana and P. persica, each of 120 genotyped individuals, have been screened for 3 years, for susceptibility to M. fructicola and to M. laxa respectively. Some genotypes of the two populations showed low or null infection the 3 years. Secondary compounds of fruit skin of all genotypes were analyzed two years by HPLC-DAD. Depending on the genotypes, 30 to 40 compounds including triterpenoids, hydroxycinnamic derivatives and flavonoids, were quantified and around 20 were identified by mass spectrometry. Among these, phenolic esters of triterpenoids were identified for the first time in peach fruit. The correlation of quantitative data between years showed their robustness. A large diversity in contents of the compounds was observed. The association and QTL analyses proved to be complementary and led to assumptions about the co-locations of loci controlling different traits, especially for compounds with differential levels in the skin of peaches and nectarines. These analyses will help deciphering the genetic control of fruit skin phenolics and triterpenoids and pave the way to the identification of the underlying genes. Detection of loci related to resistance will provide tools for the implementation of marker assisted selection. Correlations between compounds and infection traits led us to hypothesize that some compounds from peach skin could play a role in the brown rot control. The fungicide activity of these compounds is being tested in vitro.

International audience

Systematic biases in eddy covariance measurements of net ecosystem-atmosphere carbon dioxide exchange (NEE) are ubiquitous in forests when turbulence is low at night. We propose an alternative to the conventional bias correction, the friction velocity (u*) filter, by hypothesizing that these biases have two separate, concurrent causes: (1) a subcanopy CO2 storage pool that eludes typical storage measurements, creating a turbulence-dependent bias, and (2) advective divergence loss of CO2, creating a turbulence-independent bias. We correct for (1) using a simple parametric model of missing storage (MS). Prior experiments have inferred (2) directly from atmospheric measurements (DRAINO). For sites at which DRAINO experiments have not been performed or are infeasible, we estimate (2) empirically using a PAR-extrapolated advective respiration loss (PEARL) approach. We compare u* filter estimates of advection and NEE to MS-PEARL estimates at one temperate forest and two tropical forest sites. We find that for tropical forests, u* filters can produce a range of extreme NEE estimates, from long-term forest carbon emission to sequestration, that diverge from independent assessments and are not physically sustainable. Our MS model eliminates the dependence of nighttime NEE on u*, consistent with findings from DRAINO studies that nighttime advective losses of CO2 are often not dependent on the strength of turbulence. Our PEARL estimates of mean advective loss agree with available DRAINO measurements. The MS-PEARL correction to long-term NEE produces better agreement with forest inventories at all three sites. Moreover, the correction retains all nighttime eddy covariance data and is therefore more widely applicable than the u* filter approach, which rejects substantial nighttime data—up to 93% at one of the tropical sites. The full MS-PEARL NEE correction is therefore an equally defensible and more practical alternative to the u* filter, but leads to different conclusions about the resulting carbon balance. Our results therefore highlight the need to investigate which approach’s underlying hypotheses are more physically realistic.

International audience; Soil erosion processes which contribute to desertification and land degradation, constitute major environmental and social issues for the coming decades. This is particularly true in arid areas where rural populations mostly depend on soil ability to support crop production. Assessment of soil erosion across large and quite diverse areas is very difficult but crucial for planning and management of the natural resources. The purpose of this paper is to investigate a prediction model for soil vulnerability to erosion based on the use of the information contained in satellite images. Based on neural networks models, the used approach in this paper aims at checking a correlation between the digital content of satellite images and soil vulnerability factors: erosivity (R), the soil erodibility (K), and the slope length and steepness (LS); vulnerability (V) as described in the RUSLE model. Significant results have been obtained for R and K factors. This promising pilot study was conducted in South Ferlo, Senegal, a region with Sahelian environmental characteristics.

National audience; Sustainable low-carbon pork production is a priority in most pig meat producing countries. In Brazil the feed supplied to the animals is rich in nutrients and their reduction remains questioned. The objective of this study was to evaluate the effect of reducing dietary nutrient content for fattening pigs on their performance and environmental impact. The study addressed the growing-finishing phase of pig production including feed production, animal housing and manure management. Forty gilts and 40 barrows were distributed in a randomized block design with two treatments and 10 replicates per treatment. The treatments consisted in two feeding strategies with in four feeding phases in each. In the standard (ST) strategy, feed was formulated with standard Brazilian recommendations. In the low nutrient (LN) strategy, requirements were adjusted by using the InraPorc® model. Performance and excretion data were used to calculate, through life cycle assessment (LCA), the carbon emissions and the potentials of acidification and eutrophication. The functional unit was the kg of body weight gain (BWG). Both feeding strategies led to similar growth performance, with ADG of 919 g/d and FCR of 2.68 kg/kg. Carcass and meat quality were also not affected by treatments. Carbon footprint was reduced in the LN strategy in comparison with ST (2.57 versus 2.67 kg CO2-eq./kg BWG). Similar effects were observed for acidification (57.2 versus 62.3 g SO2-eq./kg BWG) and eutrophication (17.2 versus 19.0 g PO4-eq./kg BWG). Results suggest that nutritional adjustment based on prediction models is a valuable alternative to standard formulation in Brazil, which allows to improve economic results and to reduce environmental burdens without affecting technical performance.; Une production porcine durable à faible émission de carbone vers l'atmosphère est l'une des priorités dans la plupart des pays producteurs de viande du porc. Au Brésil, les aliments fournis aux animaux sont riches en nutriments et la question de la réduction des apports reste posée. L'objectif de ce travail était d'évaluer l’effet de la diminution de l’apport de nutriments sur les performances et les impacts environnementaux. L'étude a concerné la phase d'engraissement des porcs : production des aliments, élevage des animaux, gestion des effluents. Quatre-vingts porcs, femelles et mâles castrés, ont été répartis en blocs aléatoires avec deux traitements et 10 répétitions. Les traitements correspondaient à deux stratégies alimentaires avec quatre phases d'alimentation. Dans la stratégie ST (standard) les aliments sont formulés selon les recommandations Brésiliennes. Dans la stratégie BN (bas en nutriments) les besoins sont ajustés en utilisant le modèle InraPorc®. Les données de performances et d'excrétion sont utilisées pour calculer par ACV les émissions de carbone et les potentiels d’eutrophisation et d’acidification, l'unité fonctionnelle retenue étant le kg de gain de poids vif (GPV). Les deux stratégies conduisent à des performances zootechniques similaires avec en moyenne un GMQ de 919 g/j et un IC de 2,68 g/g. De même, les qualités des carcasses et des viandes ne sont pas influencées par les traitements. L'empreinte carbone est réduite avec la stratégie BN par rapport à ST (2,57 vs 2,67 kg CO2-eq./kg GPV). Des effets similaires sont observés pour l’acidification (57,2 vs 62,3 g SO2-eq./kg GPV) et l’eutrophisation (17,2 vs 19,0 g PO4-eq./kg GPV). Ces résultats indiquent que l'ajustement nutritionnel basé sur l'utilisation de modèles de prédiction est une alternative intéressante à la formulation standard au Brésil, qui permet d'atteindre les mêmes performances techniques et de qualité de viande, tout en améliorant les résultats économiques et réduisant les impacts environnementaux.